The mistreatment of local communities is a longstanding issue of Cerrejón’s mining operations. Cerrejón’s promotional materials give the impression that the company is helping the communities it has displaced, but in reality, underhand tactics were used to buy off individuals and sow internal divisions. In Roche, Cerrejón paid inhabitants extra to leave the village early, but those who stayed faced power cuts and water shortages for weeks at a time. FECODEMIGUA (the Federation of Communities Displaced by Mining in La Guajira) was formed to defend community interests and demand compensation.

In 2000, Old Oreganal was forced to move to a Cerrejón-built, semi-urban village that could not support the displaced community’s traditionally agricultural livelihood. Villagers from the village of Tabaco were evicted in 2001 for a Cerrejón expansion but, 15 years later, they were yet to be resettled. Roche, Chancleta, Tamaquitos, Manantial, Palmarito, El Descanso, Caracoli, Zarahita, and Patilla are just some of the other communities that have been devastated or simply erased by the Cerrejón coal mine.

Basic rights are casually threatened by Cerrejón, such as access to water: In 2011, the companies then operating the mine approved expansion plans that require rerouting 26 kilometres of La Guajira province’s main river, the Ranchería. This "P500 project" was vehemently opposed by locals for whom the river is their main water source and in November 2012, the project was suspended. Expansion is not off the table, although by 2021 Glencore had established a "Paris-aligned coal depletion strategy".

Threats to Indigenous territories are entwined into the project, which spans 69,000 hectares of Wayúu territory. The Wayúu share this land with people of African descent, farmers, and other Indigenous groups. Threats include cultural weakening, malnutrition and dehydration via contaminated water, and respiratory conditions partially attributed to breathing air contaminated with coal dust. Furthermore, Wayúu children are already suffering from stunted growth and a range of diseases, including chronic diarrhoea, respiratory and skin problems, vision loss, and more. From 2014-2016, these children accounted for more than 90% of childhood mortality in La Guajira, despite the Wayúu representing just 38% of La Guajira’s population.

Poor working conditions at the Cerrejón mine have frequently been highlighted, such as exploitation through cheaper labour, unhealthy working conditions, and 12-hour shifts. The Colombian coal workers' union Sintracarbón actively represents Cerrejón miners, but pro-union workers have been reportedly intimidated or replaced with cheaper, casual workers. In 2008, Sintracarbón union leader Adolfo González Montes was tortured and murdered at home in front of his children. Deteriorating working conditions prompted Sintracarbón to organise a strike in February 2013, as well as a longer, 91-day strike in 2020.

The exacerbation of COVID-19’s regional impact hit the Wayúu people particularly hard, prompting representatives to appeal against Cerrejón and its activities to the United Nations. Pervasive drought and respiratory problems in the area can be directly attributed to mining activities, both of which make combatting COVID-19 much more difficult for the Wayúu.

Significant contributions to climate change are being made by the Cerrejón coal mine. If the entirety of Cerrejón’s known coal reserves are burned, the resulting 13 billion tonnes of CO2 emissions would be equivalent to 184 years of Colombia’s national emissions. Global heating is already affecting Colombia: In 2013, The Council on Hemispheric Affairs said the surface of the Andean glaciers has shrunk by more than 90% over 10,000 years, with most of this happening since the Industrial Revolution.

Between 2002 and 2021, 559.8 million tonnes of coal were exported from Cerrejón, mostly to European and North American countries. Colombia’s per-capita carbon footprint is less than a fifth of the UK's and 11 times less than the USA’s.

Droughts and water contamination can be attributed to the mine, which draws approximately 2,700,000 litres of water from the region every day. Alongside groundwater, large volumes of water are taken from the Ranchería River. These impacts cause broad environmental damage to local rivers and habitats.